That means 70 percent of the cost was for things that are hard to measure, like Whole Foods' potential for future growth, while only 30 percent was spent on buying actual assets, like existing stores or business relationships.

"The acquisition price is being allocated mostly to goodwill, suggesting that Amazon is mostly buying the opportunity to break into this business, not because of Whole Foods' existing business," said Alan Brott, an accounting professor at Columbia University.

The heavy goodwill balance shows Amazon's confidence in turning Whole Foods into a bigger revenue driver in the future. But it also adds risk: Goodwill is tested for impairment every year, and when acquisitions don't work out as expected, companies must write it off, directly impacting the bottom line.

Peter Atwater, president at the financial research firm Financial Insyghts, said the risk of a goodwill write off is important, pointing to other tech giants that had to write off large goodwill values in recent years, such as Microsoft with Nokia or Hewlett Packard with Autonomy.

On top of that, the Whole Foods deal stands out because the 70 percent goodwill portion is higher than most other deals involving a physical store brand, Atwater said. Companies that don't own a lot of tangible assets, like software makers, tend to draw higher goodwill, but it's rare for companies in physical retail to get such high goodwill in a deal. For example, when CVS paid $1.9 billion for Target's pharmacy business in 2015, only $916 million, or 48 percent, of the deal accounted for goodwill.

"It's a very significant premium for a company that's in an old industry like grocery shopping," Atwater said. "The issue is going to be whether strategically they can create the value that is now reflected in the balance sheet in the form of that goodwill."

As a result of the Whole Foods acquisition, Amazon's goodwill balance has ballooned to $13.4 billion as of the end of 2017, the highest ever, and the first time it accounted for more than 10 percent of its total assets.

Why investors are shrugging it off

Investors, however, don't seem concerned. Traditionally, investors tend to pay less attention to goodwill write-offs because they don't hurt the company's cash flow from operations (the acquisition is already paid off, after all).

"If they do not gain as much value as anticipated from the acquisition, they might need to write some of that off, but it would be 'non-cash' in any case," Colin Sebastian, an analyst at R.W. Baird said.

Brott noted that write-offs typically don't happen too soon and that it's actually a "positive" that it'll have little impact on Amazon's profitability in the near term.

Plus, Amazon's goodwill balance is still small compared to other S&P 500 companies. At least 285 companies had goodwill over $10 billion as of the most recent quarter, while some companies like CenturyLink had goodwill that even exceeded their market cap, according to S&P Global Market Intelligence.

The historically small goodwill in part reflects Amazon's measured approach to acquiring companies. Whole Foods was by far the largest deal Amazon has made in its 25-year history, as the e-commerce company is better known for building new products than buying into new markets.

Amazon says early signs show little reason to be concerned about the deal. Amazon CFO Brian Olsavsky said in the earnings call last week that he continues to see high demand in Whole Foods stores, pointing to roughly $5 billion in sales they generated since the acquisition.

"We're continuing to be very excited about the opportunities we have to innovate with the Whole Foods and Amazon teams together," Olsavsky said.